rs2964798

Variant names:

• chr5-10788721-T-C
• rs2964798

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.841 in 152,258 control chromosomes in the GnomAD database, including 54,845 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.84 (54845 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.841 AC: 128006 AN: 152140 Hom.: 54812 Cov.: 34

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.851

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.841 AC: 128101 AN: 152258 Hom.: 54845 Cov.: 34 AF XY: 0.833 AC XY: 62054 AN XY: 74450

African (AFR) AF: 0.810 AC: 33646 AN: 41522

American (AMR) AF: 0.827 AC: 12650 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3213 AN: 3472

East Asian (EAS) AF: 0.333 AC: 1723 AN: 5176

South Asian (SAS) AF: 0.694 AC: 3354 AN: 4830

European-Finnish (FIN) AF: 0.858 AC: 9091 AN: 10600

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61536 AN: 68040

Other (OTH) AF: 0.851 AC: 1800 AN: 2116

Alfa AF: 0.878 Hom.: 218520

Bravo AF: 0.838

Asia WGS AF: 0.585 AC: 2035 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.40
PhyloP100		-0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2964798; hg19: chr5-10788833;